From 62fc6316a78bc705496796b2310cb920d8dff5e2 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 12 Aug 2010 09:59:26 +0000
Subject: [PATCH] polishing testing suite

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1056 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_test/lib/test.sh              |  19 +++++++++++++++++++
 bp_test/test/test_add_ident      |   6 +++---
 bp_test/test/test_align_seq      |   2 +-
 bp_test/test/test_analyze_gc     |   2 +-
 bp_test/test/test_analyze_vals   |   6 +++---
 bp_test/test/test_blast_seq      |  10 +++++-----
 bp_test/test/test_grab           |  20 ++++++++++----------
 bp_test/test/test_lowercase_seq  |   2 +-
 bp_test/test/test_read_blast_tab |   4 ++--
 bp_test/test/test_read_fasta     |   4 ++--
 bp_test/test/test_read_solexa    |  10 +++++-----
 bp_test/test/test_read_tab       |  16 ++++++++--------
 bp_test/test/test_swapcase_seq   |   2 +-
 bp_test/test/test_uppercase_seq  |   2 +-
 bp_test/test/test_write_blast    |   6 +++---
 bp_test/test/test_write_fasta    |   6 +++---
 bp_test/test/test_write_tab      |  12 ++++++------
 code_python/Cjung/Args.pyc       | Bin 5375 -> 5023 bytes
 18 files changed, 74 insertions(+), 55 deletions(-)

diff --git a/bp_test/lib/test.sh b/bp_test/lib/test.sh
index 84ff16c..fd2566d 100755
--- a/bp_test/lib/test.sh
+++ b/bp_test/lib/test.sh
@@ -27,6 +27,18 @@ function assert_no_diff
     local src=$1
     local dst=$2
 
+    if [ ! -f $src ]; then
+        echo_red "FAIL"
+        log "FAIL"
+        return
+    fi
+
+    if [ ! -f $dst ]; then
+        echo_red "FAIL"
+        log "FAIL"
+        return
+    fi
+
     local diff=`diff -q $src $dst`
      
     if [ "$diff" != "" ]; then
@@ -77,3 +89,10 @@ function echo_red
 
     echo -e "\033[31;38m$msg\033[0m"
 }
+
+function clean
+{
+    if [ -f "$tmp" ]; then
+        rm "$tmp"
+    fi
+}
diff --git a/bp_test/test/test_add_ident b/bp_test/test/test_add_ident
index a35b990..6e32ab6 100755
--- a/bp_test/test/test_add_ident
+++ b/bp_test/test/test_add_ident
@@ -4,12 +4,12 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -k CUSTOM_KEY -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -p PREFIX -O $tmp"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
diff --git a/bp_test/test/test_align_seq b/bp_test/test/test_align_seq
index 4266db8..61c5709 100755
--- a/bp_test/test/test_align_seq
+++ b/bp_test/test/test_align_seq
@@ -4,4 +4,4 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
diff --git a/bp_test/test/test_analyze_gc b/bp_test/test/test_analyze_gc
index 4266db8..61c5709 100755
--- a/bp_test/test/test_analyze_gc
+++ b/bp_test/test/test_analyze_gc
@@ -4,4 +4,4 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
diff --git a/bp_test/test/test_analyze_vals b/bp_test/test/test_analyze_vals
index 4fa0b2e..1e4b180 100755
--- a/bp_test/test/test_analyze_vals
+++ b/bp_test/test/test_analyze_vals
@@ -4,12 +4,12 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -o $tmp -x"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -k V0 -o $tmp -x"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -K V0 -o $tmp -x"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
diff --git a/bp_test/test/test_blast_seq b/bp_test/test/test_blast_seq
index f6b6430..5c3c52b 100755
--- a/bp_test/test/test_blast_seq
+++ b/bp_test/test/test_blast_seq
@@ -7,22 +7,22 @@ run_quiet "create_blast_index -I $in.3 -d $tmp_dir -i 'protein' -x"
 
 run "$bp -I $in.2 -d $tmp_dir/nucleotide -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in.2 -d $tmp_dir/protein -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in.4 -d $tmp_dir/nucleotide -O $tmp"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
 
 run "$bp -I $in.4 -d $tmp_dir/protein -O $tmp"
 assert_no_diff $tmp $out.4
-rm $tmp
+clean
 
 run "$bp -I $in.2 -d $tmp_dir/nucleotide -p tblastx -O $tmp"
 assert_no_diff $tmp $out.5
-rm $tmp
+clean
 
 rm -rf $tmp_dir
diff --git a/bp_test/test/test_grab b/bp_test/test/test_grab
index 4d97be0..4172e9b 100755
--- a/bp_test/test/test_grab
+++ b/bp_test/test/test_grab
@@ -4,40 +4,40 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -p SEQ -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -p SEQ,COUNT -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -P $in.pat -O $tmp"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
 
 run "$bp -I $in -p SEQ -i -O $tmp"
 assert_no_diff $tmp $out.4
-rm $tmp
+clean
 
 run "$bp -I $in -p SEQ -K -O $tmp"
 assert_no_diff $tmp $out.5
-rm $tmp
+clean
 
 run "$bp -I $in -p SEQ -V -O $tmp"
 assert_no_diff $tmp $out.6
-rm $tmp
+clean
 
 run "$bp -I $in -p SEQ -k PAT -O $tmp"
 assert_no_diff $tmp $out.7
-rm $tmp
+clean
 
 run "$bp -I $in -r a -k SEQ -O $tmp"
 assert_no_diff $tmp $out.8
-rm $tmp
+clean
 
 run "$bp -I $in -r a -k SEQ -c -O $tmp"
 assert_no_diff $tmp $out.9
-rm $tmp
+clean
 
 run "$bp -I $in -e 'SEQ_LEN<10' -O $tmp"
 assert_no_diff $tmp $out.10
-rm $tmp
+clean
diff --git a/bp_test/test/test_lowercase_seq b/bp_test/test/test_lowercase_seq
index 4266db8..61c5709 100755
--- a/bp_test/test/test_lowercase_seq
+++ b/bp_test/test/test_lowercase_seq
@@ -4,4 +4,4 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
diff --git a/bp_test/test/test_read_blast_tab b/bp_test/test/test_read_blast_tab
index cc459f8..bff0470 100755
--- a/bp_test/test/test_read_blast_tab
+++ b/bp_test/test/test_read_blast_tab
@@ -4,8 +4,8 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -i $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -i $in -n 1 -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
diff --git a/bp_test/test/test_read_fasta b/bp_test/test/test_read_fasta
index cc459f8..bff0470 100755
--- a/bp_test/test/test_read_fasta
+++ b/bp_test/test/test_read_fasta
@@ -4,8 +4,8 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -i $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -i $in -n 1 -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
diff --git a/bp_test/test/test_read_solexa b/bp_test/test/test_read_solexa
index 63a1ad0..5d0a58b 100755
--- a/bp_test/test/test_read_solexa
+++ b/bp_test/test/test_read_solexa
@@ -4,20 +4,20 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -i $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -i $in -n 1 -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -i $in -c -O $tmp"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
 
 run "$bp -i $in -s -O $tmp"
 assert_no_diff $tmp $out.4
-rm $tmp
+clean
 
 run "$bp -i $in -s -C 30 -O $tmp"
 assert_no_diff $tmp $out.5
-rm $tmp
+clean
diff --git a/bp_test/test/test_read_tab b/bp_test/test/test_read_tab
index ed2da1a..62adfcc 100755
--- a/bp_test/test/test_read_tab
+++ b/bp_test/test/test_read_tab
@@ -4,32 +4,32 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -i $in.1 -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -i $in.1 -s 1 -O $tmp"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -i $in.1 -s 1 -k ORGANISM,SEQ,COUNT -O $tmp"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
 
 run "$bp -i $in.1 -s 1 -c 2,1 -O $tmp"
 assert_no_diff $tmp $out.4
-rm $tmp
+clean
 
 run "$bp -i $in.1 -s 1 -c 2,1 -k COUNT,SEQ -O $tmp"
 assert_no_diff $tmp $out.5
-rm $tmp
+clean
 
 run "$bp -i $in.2 -O $tmp"
 assert_no_diff $tmp $out.6
-rm $tmp
+clean
 
 run "$bp -i $in.2 -n 1 -O $tmp"
 assert_no_diff $tmp $out.7
-rm $tmp
+clean
 
 run "$bp -i $in.3 -d ';' -O $tmp"
 assert_no_diff $tmp $out.8
-rm $tmp
+clean
diff --git a/bp_test/test/test_swapcase_seq b/bp_test/test/test_swapcase_seq
index 4266db8..61c5709 100755
--- a/bp_test/test/test_swapcase_seq
+++ b/bp_test/test/test_swapcase_seq
@@ -4,4 +4,4 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
diff --git a/bp_test/test/test_uppercase_seq b/bp_test/test/test_uppercase_seq
index 4266db8..61c5709 100755
--- a/bp_test/test/test_uppercase_seq
+++ b/bp_test/test/test_uppercase_seq
@@ -4,4 +4,4 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
diff --git a/bp_test/test/test_write_blast b/bp_test/test/test_write_blast
index 87ed9e0..741eb95 100755
--- a/bp_test/test/test_write_blast
+++ b/bp_test/test/test_write_blast
@@ -4,13 +4,13 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -o $tmp -x"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -c -o $tmp -x"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -Z -o $tmp.gz -x"
 gunzip $tmp.gz
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
diff --git a/bp_test/test/test_write_fasta b/bp_test/test/test_write_fasta
index 63b1ecf..68f37ce 100755
--- a/bp_test/test/test_write_fasta
+++ b/bp_test/test/test_write_fasta
@@ -4,13 +4,13 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -o $tmp -x"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -w 4 -o $tmp -x"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -w 4 -Z -o $tmp.gz -x"
 gunzip $tmp.gz
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
diff --git a/bp_test/test/test_write_tab b/bp_test/test/test_write_tab
index 21e9e35..7209fd7 100755
--- a/bp_test/test/test_write_tab
+++ b/bp_test/test/test_write_tab
@@ -4,25 +4,25 @@ source "$BP_DIR/bp_test/lib/test.sh"
 
 run "$bp -I $in -o $tmp -x"
 assert_no_diff $tmp $out.1
-rm $tmp
+clean
 
 run "$bp -I $in -c -o $tmp -x"
 assert_no_diff $tmp $out.2
-rm $tmp
+clean
 
 run "$bp -I $in -d ',' -o $tmp -x"
 assert_no_diff $tmp $out.3
-rm $tmp
+clean
 
 run "$bp -I $in -Z -o $tmp.gz -x"
 gunzip $tmp.gz
 assert_no_diff $tmp $out.4
-rm $tmp
+clean
 
 run "$bp -I $in -k 'Count' -o $tmp -x"
 assert_no_diff $tmp $out.5
-rm $tmp
+clean
 
 run "$bp -I $in -K 'Count' -o $tmp -x"
 assert_no_diff $tmp $out.6
-rm $tmp
+clean
diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index 4c39c4a68733e7fdac49e939fe26d08e98449439..795e1a5b55df1872c78e3b6dd439ae10af66b542 100644
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2.39.5